There are some enemy ships that are WAY to powerful. I have a Monquistador De Bonza Class Ship on my Swashbuckler and as far as i know it that is one powerful ship, and whenever he fights Marleyboneian Skiff class in Port Regal or some Monquistador ships in Monquista, its my ship that always end up getting turned into splinters before i can even lay a cannon ball on them, its because the enemy ends up having there weapons recharge rate or repair recharge rate timers recharge much faster before my ship's repair and weapon recharge rate timers can recharge and i end up becoming a sitting duck and get boarded way to quickly , what i recommand is that all special weapons and repair rate timers (on both bad guys and good guys ships) get set to inbetween 15 to 20 seconds for a recharge rate time, cause on my Montquistador ship i have Captain Gunn's stearing wheel and its timer is 30 or 35 seconds for a recharge rate, thats way to long for a recharge rate, my charactor or other peoples charactor might as well put up the White Flag of Surrander or a Great Big Bulls Eye on our boats before we ever lay 1 cannon ball on them. So Kingsisle you only got 2 options:

1. Make more stronger armor for all of the ships that are in the crowns shop and forget the Nautical points and Nautical leveling (cause it takes way to long to get that amount of nautical lvl to be able to use even 1 of those ship items that could be gotten from questing or the crown shop).

2. Change the recharge rate timers on all of the special weapons and repair icons too 15 to 20 second recharging rate.

And the victor will be the one who has the faster recharge rate on there special weapons and reapairs, (not on the rate of the enemy who has faster recharge timer while my ship or anybody elses hero's ship get turned into splinters recharge rate).

So far, as far as broadside combat goes, I never really had a problem.

I realize the Monquista ship you get at the end of Monquista is a very beautiful ship, but even that ship will need to be replaced.

As far as I know, you have to replace ships with stronger ones if you want to improve in broadside battles, especially in further parts of the game. Invest some savings into a stronger ship, and you will automatically do much better in broadside combat.

I do believe nautical level has something to do with this too. The lower the nautical level, the harder things seem to be. If you stop and fight a few of your current world's ships every now and then, you'll slowly level up in nautical level. Not to mention the ship parts you can collect to equip your ship with.

Actually ValeDonte the Monquista De Bonza Galleon Crown ship is not much more powerful than the free monquistan skiff you are given and is actually a skiff, itself i know a little confusing in the title of the ship. But what may be happening is your being outclassed by the ships in port royal as ships like characters do have different levels, as well as sizes. Also there are some ships in monquista that are for a higher level hidden around the edges and back. when you click on a ship you can see a small number in the upper left hand side this is the level of the enemy, perhaphs simply comparing your ships level and the level of the ship your planning on attacking may let you know if its time to upgrade your ship, not the armor and weapons but the ship itself and go from the monquistan ships to a maybe a bison frigate or galleon.

Really i think that the ship combat is quite fairly balanced as it is and would hate to see Ki change anything about it atm.
on your points of change,
1) to rid nautical levels and restrictions really is not a good idea, it is not that hard to rise in nautical if you practice, also it does make you better at ship battles to practice some, the restrictions to use certain equipment are pretty fair when you think about it, and nautical experience or levels are already not required to complete the main quest line, but to provide a nice mark of experience for a side line in themself and another sense of accomplishment.
2) there already exsist at least 3 level of armor for every ship except maybe the rafts lol at least i have not yet found any raft armor. the armor levels range from light to medium to heavy, normally and for those with crowns there is crown armor that usually is the strongest even stronger than heavy , and as an added bonus most crown gear and ships require less nautical to use than do the normal ships of equivalant power you buy for gold.
3)most enemy ships seem to use the same weapons we have access to with the same refresh